Microbiology Course Catalog

The ecology of major human, plant and animal diseases from the Black Plague to the Irish Potato Blight to AIDS. How microbes, people and other organisms interact in a changing environment, leading to new threats and controls for disease. (Gen.Ed. BS)

Hans Zinnser said, “... infectious disease is merely a disagreeable instance of a widely prevalent tendency of all living creatures to save themselves the bother of building the things they require. The plant does the work with its roots and green leaves. The cow eats the plant. Man eats both of them; and bacteria eat the man....” In the process, these interactions have fundamentally shaped our planet and ourselves. Plagues, outbreaks of diseases, have been a part of the human condition since recorded history and undoubtedly long before. In fact, disease is a part of all life for all organisms. At the same time, human activity, from agriculture to jet travel, interact with microbes and the environment to bring about plagues. Often we think of infectious diseases as the microbes that cause disease. A cold, and the virus that cause it, are thought of as the same thing. But infectious disease really describes an ecological interaction between microscopic organisms and other organisms that they use as a source of energy and nutrients, a pathogen and its host. The honors colloquium is an addendum to Microbiol 140P to further explore diseases and how they have shaped our world, how we attempt to manage them, and how we often inadvertently aid and abet them. Microbiol H140 is a 1 credit weekly discussion of readings taken from recent popular literature and press. Students will be asked to summarize the context of these articles, write a critical synopsis and participate in evaluating these synopses for publication in blog-like reader online.

Not for credit toward major. How cancer and AIDS begin and progress. The roles of individual cells, the immune system, mutations and viruses. How various physical and subtle factors influence one's chances of getting cancer. How to not get AIDS. The principles of vaccine development and why AIDS presents special difficulties. Established and new medical treatments for cancer and AIDS. What cancer and AIDS can teach us about health, healing, disease, living, and dying. (Gen.Ed. BS).

Independent Studies are general research projects arranged individually between students and faculty members. Undergraduates interested in joining a laboratory and participating in the research process should contact individual faculty members to apply to work in the faculty member’s laboratory. Generally, students earn three credits for a semester of work. Requirements for Independent Study vary and undergraduates should be sure that they understand the expectations and requirements for the credits they will earn. A Microbiology Course Override Form is required for registration in Microbiology 196 – Independent Study. This form is available in the Main Microbiology Office.

For undergraduate nursing majors only. With lab. Basic concepts of microbiology with emphasis on microbial pathogenesis and immunity. Medically important microorganisms including bacteria, fungi, and viruses and the diseases they cause. Laboratory exercises teach fundamental skills in aseptic technique, microscopy, pure culture study, and the isolation and identification of pathogenic microorganisms. (Gen.Ed. BS).

This lab course will cover basic concepts of microbiology with an emphasis on sterile technique, microscopy, isolation and cultivation of microorganisms. Identification of pathogenic organisms, antibiotic susceptibility testing, epidemiology and the detection of microbes in food will be covered. This is a 2 credit course for non-majors. It is geared towards students applying to post-graduate health care programs (physician assistant, nurse practitioner, pharmacy, etc.). Note: This course was formerly Microbiology 390B.

Independent Studies are general research projects arranged individually between students and faculty members. Undergraduates interested in joining a laboratory and participating in the research process should contact individual faculty members to apply to work in the faculty member’s laboratory. Generally, students earn three credits for a semester of work. Requirements for Independent Study vary and undergraduates should be sure that they understand the expectations and requirements for the credits they will earn. A Microbiology Course Override Form is required for registration in Microbiology 296 – Independent Study. This form is available in the Main Microbiology Office.

Overview of the microbial world including a survey of the structure, functioning, and diversity of microorganisms. Introduction to the fundamental concepts of microbial physiology, ecology, genetics, and pathogenesis.

This is a sophomore/junior level lecture course designed to provide microbiology and biology majors with a basic understanding of the mechanisms by which microorganisms, including bacteria, protozoa, fungi, and viruses cause disease, and the mechanisms of host defense against infectious microbes. Emerging and reemerging infectious diseases and development of resistance to antimicrobial agents are also discussed. Specifically, students study the innate and adaptive immune responses, cells and organs of the immune system, MHC and HLA systems, the mechanisms of antigen processing and presentation, immune dysfunction, hypersensitivities, autoimmune disorders, principles of vaccine development, HIV/AIDS and the immune system as well as the role of the immune system in cancer development. Students also learn the mechanisms used by various pathogens to evade the immune response.

Satisfies the Junior Year Writing requirement. Students develop their writing skills while completing a series of short assignments. Each participant will identify a biological topic of their choice to research and write about during the semester.

The methodology fundamental to the practice of modern biotechnology is presented. Techniques covered include establishment and manipulation of cell cultures, preparation and analysis of DNA and RNA, production of recombinant protein expression vectors, isolation, purification and characterization of proteins. Major emphasis on the student's performance of laboratory exercises which provide direct experience with each of the techniques mentioned.

This lab course will cover basic concepts of microbiology with an emphasis on sterile technique, microscopy, isolation and cultivation of microorganisms. Identification of pathogenic organisms, antibiotic susceptibility testing, epidemiology and the detection of microbes in food will be covered. This is a 1 credit course for non-majors. It is geared towards students applying to post-graduate health care programs (physician assistant, nurse practitioner, pharmacy, etc.).

A small group tutorial discussion: the role science in society combined with discussions of contemporary societal issues involving microbiology such as emerging infectious diseases and microbial biotechnology.

Independent Studies are general research projects arranged individually between students and faculty members. Undergraduates interested in joining a laboratory and participating in the research process should contact individual faculty members to apply to work in the faculty member’s laboratory. Generally, students earn three credits for a semester of work. Requirements for Independent Study vary and undergraduates should be sure that they understand the expectations and requirements for the credits they will earn. A Microbiology Course Override Form is required for registration in Microbiology 396 – Independent Study. This form is available in the Main Microbiology Office.

Program participants will undertake an honors section of independent study (research) under the direction of their research sponsor. Beyond the normal expectations for independent study students in the department, the honors section may include preparation of a review of the scientific literature in the field of the research project. (File an Honors Independent Study Contract with Commonwealth College; form may be found on the ComCol website.)

Practicum credits may be earned by undergraduates participating as undergraduate teaching assistants in laboratory and lecture courses. Students interested in being an undergraduate TA should contact the individual instructor for the course. Applications for laboratory TA’s are available at registration time in the Main Microbiology Office. A Microbiology Course Override Form is required for registration in Microbiology 398 – Practicum. This form is available in the Main Microbiology Office.

Microbial Ecology and Evolution is an advanced course supported by lectures and group discussions. This advanced course is designed to introduce upper undergraduate students to ranges of microbial life and evolutionary mechanisms to develop them. Course topics are structured to demonstrate the linkages between microbial ecology, diversity, and evolution.

Essential aspects of bacterial growth, including energy metabolism, macromolecular assemblages and functions, and the integration of metabolic processes by various regulatory mechanisms. Also the diversity of microorganisms, including origins of diversity, ecological and environmental pressures that create diversity, and how to measure diversity with examples from specific environments and microbial assemblages.

Microbial pathogens play an important role in the decline of bee colony health. The important class of microbial pathogens of bees will be investigated as well as possible solutions to problems caused by these pathogens. This course will be taught in a Team Based Learning (TBL) format. Students will learn how to work co-cooperatively as team members to complete projects and solve problems. Students learn to will use electronic data base searches, identify credible information sources, compile a reference data base using Ref Works and work collaboratively to complete team projects using Google to prepare documents and slide presentations.

Man has used breeding programs for the last 3000 years to increase yields of plants, to incorporate specific traits into farm animals and pets. Early motivation was probably first survival then commerce. Early tools were based in careful observation. Today, we have biotechnology: the ability to genetically engineer almost any organism. The ability to change and/or create any bio-molecule, drug, antibiotic, fuel or crop is almost at our fingertips. But what will make it happen? What is out motivation: survival in the face of global warming, increasing population, or to increase our own wealth through business? What are the political, social, and ethical implications of what we could do? What is doable, practical, profitable or necessary and what is a pipedream? Satisfies one of three required modules for the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.

Nearly 70% of Americans are obese or overweight. The distribution of the epidemic correlates strongly with poverty and access to high quality food. Students in this class will engage in directed literature research and discussion. Topics will start by examining risks factors for obesity including genetic, macro genetic/microbiome, societal (commercial, race, poverty). The goal of this course is to examine the obesity pandemic using a multidisciplinary approach with the aim of identifying any evidence for effective approaches to changing obesity rates. Satisfies one of three required modules for the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.

HIV rates in U.S. poverty areas rival those found in Haiti, Burundi, Ethiopia, and Angola. HIV prevalence in high-poverty neighborhoods is more than double that of the nation overall. Within high-poverty neighborhoods, prevalence among people living below the poverty line was double that of those living above it. Blacks disproportionately bear the brunt of the HIV epidemic in the US accounting for over 48% of all new cases of the disease while representing only 12% of the population. The HIV epidemic that was once thought to be a declining problem is now threatening to destroy not only the progress previously made, but also the health, well-being and potential of men and women of all races in poverty areas across the United States. Some important questions therefore need to be answered: Is race, poverty or both the driver of HIV in these communities? What should be done to stem the tide of new HIV infections in these areas of our society? This course satisfies one of the three modules required for the Integrative Experience for BA-MicBio and BS-MicBio majors.

Over 70% of the Earth’s surface is covered with the oceans, and nearly all of the life within the
ocean is microscopic. Some of these microbes are photosynthetic and form most of the base of the marine food web. These in turn are consumed by other small creatures that eventually provide food for the larger animals in the sea. Bacteria are responsible for maintaining certain chemical balances in the oceans, and themselves are food for other microbes. Understanding how life is sustained in our oceans is vital for coastal human populations that rely on the sea for food. Other people turn to marine microbes for new biotechnologies, or hope that by understanding them we might understand our own planet’s climate history and how marine microbes will respond to global warming and ocean acidification. Satisfies one of the three required modules for the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.

Drug resistance is a major problem that complicates the treatments of infectious diseases. It is a consequence of genetic changes in a microbe, and molecular mechanisms vary widely including mutations of target enzymes, increased expression of efflux pump, horizontal transfer of resistance gene, and induction of inactivating enzymes. While understanding the molecular mechanisms of drug resistance is critical to introduce next generation drugs, we also need effort to fill in the gap between basic science discoveries and tackling socioeconomical issues associated with drug resistance such as noncompliance of patients, overuse of antibiotics, and lack of governmental support. Is discovering new antibiotics the only thing scientists can do? How can we reduce the chances of developing drug-resistant microbes? Are we really reducing the burden of infectious diseases by introducing more antibiotics? Students will have opportunities to gain wider integral perspectives on how to tackle infectious diseases. Satisfies one of three required modules for the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.

Students will engage in meaningful literature research and dialogue about whether organic standards are meeting the needs of both environmental and community sustainability. We will also consider the benefits of sustainable agriculture, both in the sense of conservation of land and soil as limiting natural resources, as well as the sense of community with the farm and food production as the center of family and local community life. In exploring these wide-ranging issues, students will have the opportunity to reflect on and integrate their Gen Ed learning experience from various courses as well as practice Gen Ed learning objectives at a more advanced level as they seek meaningful solutions to complex and ever evolving societal problems. Students will work in small groups to explore these solutions allowing them to participate in shared learning experiences as they apply prior knowledge from various Gen Ed courses and social experiences to solve challenging real-world problems. Satisfies one of three required modules of the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.

The vast majority of Earth's biodiversity is microbial. Microorganisms are directly involved in the ecosystem services on which all of life depends. They interact intimately with other organisms and yet we know much less about their biodiversity than we do for plants and animals. Our lack of understanding of the interactions and feedbacks of microbial biodiversity is troubling, given the high rates of environmental change that the Earth is currently experiencing, including man-made global climate change. Satisfies one of three required modules for the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.

Neglected tropical diseases (NTDs) are a set of infectious diseases arising from a diverse group of parasitic worms, bacteria, and vector-borne protozoa that affect an estimated 1.4 billion people worldwide. These diseases affect the world’s most vulnerable populations, almost exclusively poor and powerless people living in rural areas and urban slums of low-income countries. NTDs coexist with poverty because they thrive where access to clean water and sanitation are limited and people live without protection from insects that transmit disease. They also contribute to poverty since they can impair intellectual development in children, reduce school enrollment, and hinder economic productivity by limiting the ability of infected individuals to work. Current control efforts focus primarily on mass drug administration (MDA) to treat the seven most common NTDs and has become one of the most cost effective global health programs to treat multiple diseases at once, in large part because major pharmaceutical companies are donating the needed medicines for free. End 7 is a global campaign to deworm the world and bring an end to 7 of the NTDs. Important questions exist related to this global health strategy: what might be the long-term benefits (and possible detriments) to a sustained global deworming effort? What other measures should be implemented in combination with MDA for sustained control? Satisfies one of the three required modules for the Integrative Experience requirement for BA-MicBio or BS-MicBio majors.

In this course, we will explore the field of quorum sensing and cellular communication, focusing on strategies microbes have developed to sense neighboring cells and regulate biological processes. A specific emphasis will be placed on processes of biomedical importance and environmental relevance as well as effective strategies to manipulate of alter these processes to benefit mankind. Students will develop two presentations. Satisfies one of the three required modules for the Integrative Experience requirement for BS-MicBio majors.In this course, we will explore the field of quorum sensing and cellular communication, focusing on strategies microbes have developed to sense neighboring cells and regulate biological processes. A specific emphasis will be placed on processes of biomedical importance and environmental relevance as well as effective strategies to manipulate of alter these processes to benefit mankind. Students will develop two presentations. Satisfies one of the three required modules for the Integrative Experience requirement for BS-MicBio majors.

The honors project consists of completing and presenting the original research undertaken. The presentation will include but not be limited to an abstract suitable for publication and a research summary in the form of a poster appropriate for presentation at a scientific meeting. A Departmental Poster Presentation Session will be held at the end of the semester. Honors students are also encouraged to present their results at local or national scientific meetings. Students must also complete the Capstone Manuscript requirement of Commonwealth College. File an Independent Capstone Contract with Commonwealth College.

Original microbiological research carried out under the direction of the research sponsor. The honors student will take an active role in the experimental design of the research project. While it is not expected that undergraduate honors student will be fully capable of initiating original research on their own it is hoped that participation in the design and implementation of a research project will help the student acquire the necessary skills to carry out independent research. Independent Capstone Contract and Research Proposal with Commonwealth College; form and proposal information may be found on the ComCol website.

This laboratory course is designed to help students become familiar with and proficient in the performance of protocols in cellular immunology, immunochemistry and clinical serology. These experiments are designed to introduce the student to the fundamentals of laboratory work in the field of immunology. The laboratory experience is designed to be closely reflect that of a modern immunology lab, taking into consideration the limitations of time and available state-of-the-art equipment. Students will also have relevant lectures in these topic areas to assist in learning the principles governing each of these important protocols. This will be accomplished over the course of the semester by antibody isolation and purification using salt precipitation, ion exchange chromatography and dialysis. Purified IgG antibody molecules will be cleaved by specific enzymes in order to study the protein biochemistry of antibodies, and size exclusion or molecular sieving column chromatography will be used to isolate fragments for further analysis. Students will become proficient in the use of spectrophotometers, perform SDS-PAGE, Western blot analysis, immunoprecipitation, enzyme-linked immunosorbent assays, and immunofluorescence staining. The student will also perform comparative proteomics using immunology techniques as well as classic serological assays including the immunodiffusion (Ouchterlony technique) and blood typing. Anatomy of the lymphatic system will be explored using a mouse model. Specifically, student will perform mouse dissection, lymph node examination, and isolation of lymphocytes from the mouse spleen and thymus. In addition students will perform assays to determine protein concentration, and solidify their skills in light and fluorescence microscopy. Finally, the student will be exposed to cellular immunology, including differential leukocyte counts, mammalian histology and immunohistopathology, identification and enumeration of mouse and human leukocytes and Flow Cytometric analysis of lymphocyte subpopulations. We will take a field trip to Baystate Medical Center to visit the transfusion medicine and immunology departments where students will get the opportunity to observe many of the protocols they learned in class in use within a clinical setting and have ample opportunity to interact with the director of transfusion medicine and a transfusion medicine education specialist. Students will be evaluated via quizzes, class participation, competence at the lab bench, demonstrated independence and critical thinking along with lab reports written in theUniform Requirements for Manuscripts Submitted to Biomedical Journals format with an IMRAD structure, ready to be published.

Laboratory procedures in clinical and diagnostic bacteriology including: i) culture and characteristics of most commonly encountered pathogenic bacteria; ii) recommended procedures for their cultivation and isolation from clinical material; iii) conventional and rapid methods for detection and identification; iv) prescribed tests for the susceptibility of bacteria to antibiotics.

Semester(s) offered: Fall

Prerequisites: Must have completed MICROBIO 312 with a B- or better; MICROBIO 312 and 552 may be taken concurrently only by consent of instructor

This course covers a detailed analysis of the molecular mechanisms that control the maintenance, expression, and evolution of prokaryotic and eukaryotic genomes. The topics covered in lectures and readings of relevant literature include DNA replication, transcription, gene regulation, genetic recombination, and translation. Class format will include lectures, journal clubs, presentations and group discussions.

Microbial Biotechnology is a laboratory course supported by lectures and demonstrations. This advanced course is designed to introduce graduate level students to traditional and molecular methods strategically applied to problems related to microbial biotechnology and environmental microbiology. Course topics cover a wide range of subjects from the diversity of microbial life to biodegradation. Seven general areas are emphasized: (1) Statistical sampling and chemical and physical site characterization, (2) biomass determination and cell counts, (3) enrichment techniques, (4) microbial activity measurements, (5) single cell detection in situ, (6) sequence analysis and phylogenetic analysis followed by probe design, and (7) other modern techniques of environmental microbiology.

Methodology and principles of modern molecular genetics. Microbial genetics combining classical techniques with bacteriophages and bacteria with modern PCR and recombinant DNA experiments. Introduction to genomic, structural analysis using computer methods and fluorescence microscopy in bacteria. Designed to help students learn techniques and analyze results.

Classical and modern parasitology concentrating on protozoan and worm parasites of major medical/veterinary importance. Topics include basic principles of parasitology, life cycles, epidemiology, host-parasite interactions, drug treatments and vector control programs, along with information on the basic biology, biochemistry, and genetics of selected parasites.

Examination of all aspects related to the third Domain of life, the Archaea. New and recent papers on the physiology, ecology, biotechnological applications and evolution of archaea are discussed, as well as papers on the application of this information to biogeochemistry, early Earth history, and the search for life beyond Earth. A basic understanding of microbiology is recommended.

How Microorganisms interact with each other and with their environment. Microbial distribution and activities in natural systems, and their importance to ecosystem function and environmental quality. Extreme habitats; habitat-specific forces; microbial activity; microbial transformations and their impact on different environments; species diversity, detection, and control of microorganisms; and associations with higher organisms. Each basic principle followed by applied and environmental case studies. Modern techniques of environmental microbiology graduate students write an independent research proposal.

Main aspects of microbial growth, energy and biosynthesis pathways, metabolic regulation and integration of pathways into a coherent system. Emphasis on physiological diversity, global control systems governing the adaptation of microorganisms to different environmental conditions, and emerging methodologies.

The Applied Molecular Biotechnology Laboratory (AMBL) is a requisite course for the MS concentration in Applied Molecular Biology. AMBL combines hands on laboratory training with independent research experience to train students in the latest techniques and concepts of molecular biology and biochemistry. Recombinant DNA technology is the primary focus of the first semester. Topics covered include nucleic acid isolation, genomics, quantitative PCR and RT-PCR, southern and northern blot analysis, and computational biological analyses. Protein expression, purification, and detection are the focus of the second semester. Topics covered include prokaryotic and eukaryotic protein expression systems, column chromatography, proteomics, western blot analysis, enzymatic assay, and microscopic analysis. Throughout the year-long course, students will develop critical thinking skills and gain valuable research experience, all while working on real world problems and preparing for careers in the biotechnology and pharmaceutical industries.

Fundamental and advanced topics in the molecular genetics of micro-organisms covered through lecture and discussion of the literature. Topics vary depending on the instructor. Prerequisites: basic coursework in biochemistry and genetics. Credit, 3

A 10 week laboratory work participation. It will occur after the second semester of campus classes (summer). Students are required to actively work in a research or a production laboratory to gain hands on work experience. All work should include some responsibility. It is preferred that students work on a research projects. This can be fulfilled by a traditional internship at a company (paid), at an academic institution (unpaid) or by a full time career based job. Acceptable performance is evaluated by the supervising scientist. A final grade will be assigned by the program director.

Studies the active subsurface iosphere in sedimentary basins, to advance understanding of: 1) the forms of metabolic processes employed by such populations, and limits on the activity of subsurface microbial communities; 2) the origin, survival, and dormancy of slowly-growing subsurface microorganisms far removed from earth surface influences; 3) the geochemical, mineralogical and molecular signatures that subsurface organisms may imprint on rocks and sediments; and 4) the impact that active modern populations may have on overprinting of paleoenvironmental signatures preserved in ancient sediments and rocks.

Presentations an discussions of important microbial ecology research papers from the current literature. Fundamental questions in microbial ecology include: what are the drivers of community assembly? How do microbial functions scale? How does mass flow between species, and what factors regulate this? How can we predict or engineer community function? We will discuss microbial communities from a variety of natural and manufactured environments, with emphasis on new strategies to test hypothesis-driven microbial ecology research.

Critical review of the scientific literature is an integral part of scientific research, and both students and faculty benefit greatly from the discussions originating from these reviews.This well organized journal club entails critical review of the scientific literature deemed beneficial and relevant to both students and immunology faculty. Students make one presentation of a journal article from a reputable immunology-related journal with the advice and final approval from an immunology faculty member. Topics mayinclude, but are not limited to molecular immunology, programmed cell death, virus immunology, infection and defense, cellular immunology and receptor-mediated signaling.

Explores through current primary literature some of the complex processes used by microbial pathogens to establish themselves in a host and to gain nutrients, subsequently causing host cell damage and disease, and to evade the host's defense. Includes discussion of the modern molecular biology, genetics, and biochemistry tools to study these processes.